Valloric, my apologies if I've just missed it, but is there any way to apply calibre's "Series" (and series number) meta-info from within Sigil? Applying the tags after the fact from within calibre appears to only create a database entry, rather than embedding the info within the file.
My preference is to generate *.epub files that will sort and organize properly, regardless of which database (calibre, iTunes, etcetera) receives them. I've already found a quick way to prep files for iTunes
, but no automated solution to prepping files for calibre yet.